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Orphan Crops Browser: a bridge between model and orphan crops.

Claire Lessa Alvim Kamei1,2, Edouard I Severing3,4, Annemarie Dechesne1

  • 1Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Molecular Breeding : New Strategies in Plant Improvement
|January 23, 2016
PubMed
Summary

Researchers developed the Orphan Crops Browser to help study orphan crops using next-generation sequencing data. This tool aids in identifying gene candidates and designing primers for expression studies, simplifying bioinformatics for breeders.

Keywords:
Bioinformatics toolBreeding targetsDe novo transcriptomeOrphan cropsOrthologous genes

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Crop science

Background:

  • Orphan crops are understudied due to economic factors or complex genomes.
  • De novo transcriptome assembly offers a viable approach for studying these crops.
  • Existing bioinformatics tools are insufficient for effectively analyzing transcriptome data for molecular breeders.

Purpose of the Study:

  • To develop a user-friendly bioinformatics tool, the Orphan Crops Browser, for analyzing de novo transcriptome data from orphan crops.
  • To enable molecular breeders with limited bioinformatics expertise to study orphan crops.
  • To facilitate the identification of candidate transcripts and primer design for gene expression studies.

Main Methods:

  • Development of the Orphan Crops Browser, a web-based tool.
  • Utilizing phylogenetic relationships for orthologous sequence data analysis.
  • Designing specific and degenerate primers for expression studies.
  • Application of the browser to identify lignin biosynthetic gene orthologues in Miscanthus sinensis.

Main Results:

  • The Orphan Crops Browser was successfully used to identify 17 putative lignin biosynthetic gene orthologues in Miscanthus sinensis.
  • Expression studies revealed a negative correlation between lignin content and gene expression in Miscanthus sinensis stem internodes.
  • The findings align with recent studies in maize and other crops regarding lignification.

Conclusions:

  • The Orphan Crops Browser is a valuable tool for the molecular breeding of orphan crops.
  • The tool simplifies the analysis of de novo transcriptome data, making it accessible to non-bioinformaticians.
  • The study provides insights into lignification pathways in Miscanthus sinensis, contributing to orphan crop research.